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- PDB-1hya: HYALURONIC ACID, STRUCTURE OF A FULLY EXTENDED 3-FOLD HELICAL SOD... -

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Entry
Database: PDB / ID: 1hya
TitleHYALURONIC ACID, STRUCTURE OF A FULLY EXTENDED 3-FOLD HELICAL SODIUM SALT AND COMPARISON WITH THE LESS EXTENDED 4-FOLD HELICAL FORMS
Components
  • (0) x 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid
  • (1) x SODIUM ION
  • (2) x water
KeywordsTEXTURE OF CONNECTIVE TISSUE
Function / homologypolysac:dglcpnacb1-4dglcpaa1-3dglcpnacb1-4dglcpaa1-3dglcpnacb1-4dglcpaa1-roh:
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsArnott, S.
Citation
Journal: J.Mol.Biol. / Year: 1975
Title: Hyaluronic acid: structure of a fully extended 3-fold helical sodium salt and comparison with the less extended 4-fold helical forms.
Authors: Winter, W.T. / Smith, P.J. / Arnott, S.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1978
Title: Lals, a Linked-Atom Least-Squares Reciprocal-Space Refinement System Incorporating Stereochemical Restraints to Supplement Sparse Diffraction Data
Authors: Smith, P.J.C. / Arnott, S.
#2: Journal: J.Mol.Biol. / Year: 1975
Title: Hyaluronic Acid, Molecular Conformations and Interactions in Two Sodium Salts
Authors: Guss, J.M. / Hukins, D.W.L. / Smith, P.J.C. / Winter, W.T. / Arnott, S. / Moorhouse, R. / Rees, D.A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 20, 1977Processing site: BNL
Revision 1.0May 17, 1978Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,2254
Polymers0
Non-polymers1,2254
Water21612
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)11.700, 11.700, 28.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-992-

HOH

21A-996-

HOH

31A-1000-

HOH

DetailsTHE SIX-RESIDUE CHAIN SEGMENT GIVEN HERE WAS GENERATED FROM THE PUBLISHED TWO-RESIDUE SEGMENT BY APPLICATION OF THE THREE-FOLD SCREW AXIS LOCATED AT (2/3, 1/3, Z). THE EQUIPOINTS (IN FRACTIONAL COORDINATES) WHICH WERE USED ARE (X, Y, Z), (Y-X+1, -X+1, Z+1/3), (-Y+1, X-Y, Z+2/3) .

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Components

#1: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 1155.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpAa1-3DGlcpNAcb1-4DGlcpAa1-3DGlcpNAcb1-4DGlcpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122A-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-1-2-1-2/a4-b1_b3-c1_c4-d1_d3-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpA]{[(4+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#2: Chemical ChemComp-NA / SODIUM ION / Sodium


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE GLUCURONIC ACID-GLUCOSAMINE LINKAGE IS BETA(1,3) AND THE GLUCOSAMINE-GLUCURONIC ACID LINKAGE IS BETA(1,4).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

Software
NameVersionClassification
LINKED-ATOMLEAST-SQUARES MODEL-BUILDING PROCEDURErefinement
LALSrefinement
RefinementHighest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 81 12 93

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